Starting phenix.real_space_refine on Fri Mar 15 15:21:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkw_32570/03_2024/7wkw_32570_trim_updated.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3938 2.51 5 N 940 2.21 5 O 998 1.98 5 H 6138 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6006 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.48 Number of scatterers: 12056 At special positions: 0 Unit cell: (80.845, 121.693, 71.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 998 8.00 N 940 7.00 C 3938 6.00 H 6138 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 72.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'B' and resid 4 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.807A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.760A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 144 through 164 Processing helix chain 'B' and resid 476 through 491 Processing helix chain 'B' and resid 495 through 513 Processing helix chain 'B' and resid 519 through 546 removed outlier: 4.214A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 4.262A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 584 through 594 removed outlier: 4.004A pdb=" N ARG B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 613 through 639 removed outlier: 4.738A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing helix chain 'A' and resid 4 through 29 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 36 through 59 removed outlier: 4.811A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.764A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 144 through 164 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 476 through 491 Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.208A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 4.262A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 594 removed outlier: 3.978A pdb=" N ARG A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 613 through 639 removed outlier: 4.727A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 174 through 177 removed outlier: 4.267A pdb=" N SER B 174 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 177 removed outlier: 4.270A pdb=" N SER A 174 " --> pdb=" O LEU A 202 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6132 1.02 - 1.21: 8 1.21 - 1.41: 2426 1.41 - 1.61: 3560 1.61 - 1.81: 78 Bond restraints: 12204 Sorted by residual: bond pdb=" ND2 ASN A 112 " pdb="HD22 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 112 " pdb="HD21 ASN A 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 112 " pdb="HD21 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 112 " pdb="HD22 ASN B 112 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C12 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 1.347 1.458 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 308 107.05 - 113.79: 14717 113.79 - 120.52: 4072 120.52 - 127.26: 2985 127.26 - 133.99: 78 Bond angle restraints: 22160 Sorted by residual: angle pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 108.41 102.31 6.10 1.61e+00 3.86e-01 1.43e+01 angle pdb=" N ASN A 112 " pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 108.41 102.38 6.03 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 113.71 111.37 2.34 9.50e-01 1.11e+00 6.09e+00 angle pdb=" N VAL B 173 " pdb=" CA VAL B 173 " pdb=" C VAL B 173 " ideal model delta sigma weight residual 113.71 111.40 2.31 9.50e-01 1.11e+00 5.91e+00 angle pdb=" N TYR A 145 " pdb=" CA TYR A 145 " pdb=" C TYR A 145 " ideal model delta sigma weight residual 111.36 108.85 2.51 1.09e+00 8.42e-01 5.31e+00 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5150 16.79 - 33.58: 403 33.58 - 50.37: 101 50.37 - 67.15: 54 67.15 - 83.94: 2 Dihedral angle restraints: 5710 sinusoidal: 3066 harmonic: 2644 Sorted by residual: dihedral pdb=" CA PHE A 49 " pdb=" C PHE A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE B 49 " pdb=" C PHE B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 29 " pdb=" CD ARG B 29 " pdb=" NE ARG B 29 " pdb=" CZ ARG B 29 " ideal model delta sinusoidal sigma weight residual -180.00 -135.46 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 765 0.038 - 0.076: 165 0.076 - 0.115: 54 0.115 - 0.153: 4 0.153 - 0.191: 2 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASN B 112 " pdb=" N ASN B 112 " pdb=" C ASN B 112 " pdb=" CB ASN B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ASN A 112 " pdb=" N ASN A 112 " pdb=" C ASN A 112 " pdb=" CB ASN A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA PRO A 16 " pdb=" N PRO A 16 " pdb=" C PRO A 16 " pdb=" CB PRO A 16 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 987 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 112 " -0.080 2.00e-02 2.50e+03 7.86e-02 9.27e+01 pdb=" CG ASN B 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 112 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN B 112 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 112 " 0.110 2.00e-02 2.50e+03 pdb="HD22 ASN B 112 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 112 " -0.077 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 112 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 112 " 0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN A 112 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 112 " 0.106 2.00e-02 2.50e+03 pdb="HD22 ASN A 112 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 569 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 570 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.027 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 653 2.21 - 2.80: 24715 2.80 - 3.40: 33142 3.40 - 4.00: 42912 4.00 - 4.60: 67426 Nonbonded interactions: 168848 Sorted by model distance: nonbonded pdb=" O GLU B 178 " pdb="HH12 ARG B 489 " model vdw 1.607 1.850 nonbonded pdb=" HH TYR A 18 " pdb=" O MET A 624 " model vdw 1.607 1.850 nonbonded pdb=" O GLU A 178 " pdb="HH12 ARG A 489 " model vdw 1.608 1.850 nonbonded pdb=" HH TYR B 18 " pdb=" O MET B 624 " model vdw 1.609 1.850 nonbonded pdb=" O LEU B 23 " pdb=" HG SER B 27 " model vdw 1.615 1.850 ... (remaining 168843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 3.730 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 42.060 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 6066 Z= 0.270 Angle : 0.565 6.626 8266 Z= 0.297 Chirality : 0.038 0.191 990 Planarity : 0.005 0.048 998 Dihedral : 13.100 83.944 2134 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 746 helix: 1.70 (0.22), residues: 560 sheet: -0.12 (0.79), residues: 42 loop : -0.65 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.002 0.001 HIS B 57 PHE 0.007 0.001 PHE A 45 TYR 0.005 0.001 TYR B 635 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 1.8612 time to fit residues: 253.1299 Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 6066 Z= 0.330 Angle : 0.728 7.599 8266 Z= 0.368 Chirality : 0.043 0.144 990 Planarity : 0.006 0.069 998 Dihedral : 5.459 30.558 816 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.66 % Allowed : 8.15 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 746 helix: 1.29 (0.21), residues: 558 sheet: -0.16 (0.74), residues: 42 loop : -0.67 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 506 HIS 0.005 0.001 HIS B 57 PHE 0.016 0.002 PHE B 56 TYR 0.010 0.002 TYR B 25 ARG 0.005 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.880 Fit side-chains REVERT: B 21 MET cc_start: 0.7037 (ttp) cc_final: 0.6680 (ttp) REVERT: B 159 MET cc_start: 0.6760 (mtp) cc_final: 0.6548 (mtp) REVERT: B 162 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.4931 (mtp) REVERT: B 624 MET cc_start: 0.7000 (tpt) cc_final: 0.5685 (tpt) REVERT: A 21 MET cc_start: 0.7097 (ttp) cc_final: 0.6646 (ttp) REVERT: A 159 MET cc_start: 0.6758 (mtp) cc_final: 0.6550 (mtp) REVERT: A 162 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.4924 (mtp) REVERT: A 624 MET cc_start: 0.7176 (tpt) cc_final: 0.6036 (tpt) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 1.6719 time to fit residues: 200.4547 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6066 Z= 0.222 Angle : 0.553 4.994 8266 Z= 0.286 Chirality : 0.039 0.140 990 Planarity : 0.005 0.047 998 Dihedral : 5.631 31.988 816 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.76 % Allowed : 11.76 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 746 helix: 1.49 (0.22), residues: 558 sheet: 0.12 (0.73), residues: 42 loop : -0.97 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 506 HIS 0.003 0.001 HIS B 57 PHE 0.007 0.001 PHE B 152 TYR 0.010 0.001 TYR A 635 ARG 0.002 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7962 (mtt) cc_final: 0.7750 (mtt) REVERT: B 562 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6885 (mmt) REVERT: B 624 MET cc_start: 0.7340 (tpt) cc_final: 0.5753 (tpt) REVERT: A 562 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6897 (mmt) REVERT: A 624 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6035 (tpt) outliers start: 24 outliers final: 4 residues processed: 100 average time/residue: 1.7286 time to fit residues: 184.9545 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 624 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 522 GLN A 140 GLN A 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6066 Z= 0.269 Angle : 0.631 6.461 8266 Z= 0.320 Chirality : 0.040 0.140 990 Planarity : 0.005 0.049 998 Dihedral : 5.359 30.338 816 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.66 % Allowed : 13.64 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 746 helix: 1.40 (0.22), residues: 554 sheet: -0.02 (0.71), residues: 42 loop : -1.05 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 506 HIS 0.003 0.001 HIS A 187 PHE 0.011 0.002 PHE B 566 TYR 0.005 0.001 TYR A 25 ARG 0.003 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 562 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: B 624 MET cc_start: 0.7642 (tpt) cc_final: 0.6093 (tpt) REVERT: A 562 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7145 (mmt) REVERT: A 624 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6345 (tpt) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 1.9545 time to fit residues: 189.6175 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6066 Z= 0.214 Angle : 0.533 6.649 8266 Z= 0.276 Chirality : 0.038 0.139 990 Planarity : 0.005 0.048 998 Dihedral : 5.601 34.512 816 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.35 % Allowed : 13.48 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 746 helix: 1.51 (0.22), residues: 554 sheet: 0.12 (0.71), residues: 42 loop : -1.03 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.003 0.001 HIS A 187 PHE 0.008 0.001 PHE B 45 TYR 0.009 0.001 TYR B 635 ARG 0.001 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7914 (ttp) cc_final: 0.7560 (ttt) REVERT: B 624 MET cc_start: 0.7713 (tpt) cc_final: 0.6176 (tpt) REVERT: A 21 MET cc_start: 0.7908 (ttp) cc_final: 0.7426 (ttt) REVERT: A 624 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6400 (tpt) outliers start: 15 outliers final: 6 residues processed: 91 average time/residue: 2.0090 time to fit residues: 194.1172 Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6066 Z= 0.231 Angle : 0.557 7.233 8266 Z= 0.286 Chirality : 0.038 0.137 990 Planarity : 0.005 0.050 998 Dihedral : 5.599 35.596 816 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.66 % Allowed : 13.79 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 746 helix: 1.52 (0.22), residues: 554 sheet: 0.18 (0.70), residues: 42 loop : -1.09 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 506 HIS 0.003 0.001 HIS A 187 PHE 0.008 0.002 PHE B 566 TYR 0.007 0.001 TYR A 635 ARG 0.003 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8079 (ttp) cc_final: 0.7722 (ttt) REVERT: B 520 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7047 (mt) REVERT: B 624 MET cc_start: 0.7729 (tpt) cc_final: 0.6268 (tpt) REVERT: A 21 MET cc_start: 0.8054 (ttp) cc_final: 0.7562 (ttt) REVERT: A 624 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6605 (tpt) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 1.9851 time to fit residues: 181.4313 Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.8305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6066 Z= 0.221 Angle : 0.548 8.326 8266 Z= 0.283 Chirality : 0.038 0.136 990 Planarity : 0.005 0.050 998 Dihedral : 5.731 36.823 816 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.19 % Allowed : 15.20 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.31), residues: 746 helix: 1.45 (0.21), residues: 554 sheet: 0.07 (0.71), residues: 42 loop : -1.08 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.003 0.001 HIS A 187 PHE 0.009 0.001 PHE B 45 TYR 0.009 0.001 TYR A 635 ARG 0.003 0.001 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8091 (ttp) cc_final: 0.7745 (ttt) REVERT: B 127 GLU cc_start: 0.6454 (mp0) cc_final: 0.6254 (mm-30) REVERT: B 624 MET cc_start: 0.7807 (tpt) cc_final: 0.6387 (tpt) REVERT: A 21 MET cc_start: 0.8116 (ttp) cc_final: 0.7593 (ttt) REVERT: A 472 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6678 (t0) REVERT: A 624 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6634 (tpt) outliers start: 14 outliers final: 6 residues processed: 89 average time/residue: 2.1470 time to fit residues: 201.8505 Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.8473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6066 Z= 0.188 Angle : 0.531 8.521 8266 Z= 0.272 Chirality : 0.037 0.132 990 Planarity : 0.005 0.048 998 Dihedral : 5.315 31.543 816 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.88 % Allowed : 15.67 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.31), residues: 746 helix: 1.56 (0.22), residues: 558 sheet: 0.03 (0.70), residues: 42 loop : -0.83 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 506 HIS 0.001 0.001 HIS B 187 PHE 0.008 0.001 PHE B 45 TYR 0.008 0.001 TYR A 635 ARG 0.002 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 21 MET cc_start: 0.8137 (ttp) cc_final: 0.7606 (ttt) REVERT: B 127 GLU cc_start: 0.6496 (mp0) cc_final: 0.6191 (mm-30) REVERT: B 624 MET cc_start: 0.7788 (tpt) cc_final: 0.6327 (tpt) REVERT: A 21 MET cc_start: 0.8124 (ttp) cc_final: 0.7611 (ttt) REVERT: A 624 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6594 (tpt) outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 2.1497 time to fit residues: 197.9235 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.8577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6066 Z= 0.180 Angle : 0.528 9.605 8266 Z= 0.269 Chirality : 0.037 0.132 990 Planarity : 0.005 0.048 998 Dihedral : 5.076 27.542 816 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.72 % Allowed : 15.36 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.31), residues: 746 helix: 1.62 (0.22), residues: 558 sheet: 0.04 (0.70), residues: 42 loop : -0.81 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.001 0.001 HIS A 57 PHE 0.007 0.001 PHE B 45 TYR 0.009 0.001 TYR A 635 ARG 0.002 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.8121 (ttp) cc_final: 0.7715 (ttt) REVERT: B 127 GLU cc_start: 0.6474 (mp0) cc_final: 0.6174 (mm-30) REVERT: B 624 MET cc_start: 0.7795 (tpt) cc_final: 0.6299 (tpt) REVERT: A 127 GLU cc_start: 0.6374 (mp0) cc_final: 0.6173 (mm-30) REVERT: A 472 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6745 (t0) REVERT: A 624 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6668 (tpt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 2.1422 time to fit residues: 190.5339 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6066 Z= 0.144 Angle : 0.508 10.243 8266 Z= 0.256 Chirality : 0.036 0.130 990 Planarity : 0.005 0.045 998 Dihedral : 4.428 17.274 816 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.10 % Allowed : 15.67 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.32), residues: 746 helix: 1.90 (0.22), residues: 558 sheet: -0.02 (0.68), residues: 42 loop : -0.72 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 144 HIS 0.003 0.000 HIS A 57 PHE 0.006 0.001 PHE B 45 TYR 0.007 0.001 TYR A 635 ARG 0.001 0.000 ARG A 489 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 486 MET cc_start: 0.7156 (mmm) cc_final: 0.6691 (mmm) REVERT: B 624 MET cc_start: 0.7777 (tpt) cc_final: 0.6221 (tpt) REVERT: A 486 MET cc_start: 0.7151 (mmm) cc_final: 0.6689 (mmm) REVERT: A 624 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6681 (tpt) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 2.1848 time to fit residues: 191.7403 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146538 restraints weight = 17541.230| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.15 r_work: 0.3560 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.8728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6066 Z= 0.173 Angle : 0.518 9.326 8266 Z= 0.264 Chirality : 0.036 0.132 990 Planarity : 0.005 0.046 998 Dihedral : 4.566 17.795 816 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.25 % Allowed : 15.52 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.32), residues: 746 helix: 1.83 (0.22), residues: 558 sheet: -0.10 (0.69), residues: 42 loop : -0.75 (0.58), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.001 0.000 HIS A 187 PHE 0.007 0.001 PHE B 45 TYR 0.008 0.001 TYR A 635 ARG 0.002 0.000 ARG B 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4584.25 seconds wall clock time: 80 minutes 30.22 seconds (4830.22 seconds total)